[gmx-users] protein-ligand simmulation

[Justin Lemkul]

On 4/26/17 9:22 AM, Aman Deep wrote:
> I am trying to simulate protein-ligand complex simulation and I have
> followed the tutorial of Bevan lab but in energy minimization step it gives
> me this error...
>
> *Fatal error:*
> *Atom type CH1 not found*
> *For more information and tips for troubleshooting, please check the
> GROMACS*
>
> I have made drug.itp file from prodrug and include it in topol.top file but
> still it is giving me the error...

Likely you're trying to mix and match force fields, as CH1 is a valid type for 
any GROMOS parameter set.

But don't use PRODRG; as the tutorial warns (and as I am on record a million 
times over saying) the quality of those topologies is inadequate for MD 
simulations.  You'll have to correct it significantly or use a better source of 
parameters (manual reparametrization, ATB server, etc).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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